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Diffstat (limited to 'var/spack/repos/builtin/packages/roary/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/roary/package.py | 71 |
1 files changed, 71 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/roary/package.py b/var/spack/repos/builtin/packages/roary/package.py new file mode 100644 index 0000000000..f17d54ff32 --- /dev/null +++ b/var/spack/repos/builtin/packages/roary/package.py @@ -0,0 +1,71 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack.package import * + + +class Roary(Package): + """Rapid large-scale prokaryote pan genome analysis""" + + homepage = "https://github.com/sanger-pathogens/Roary" + url = "https://github.com/sanger-pathogens/Roary/archive/refs/tags/v3.13.0.tar.gz" + + version("3.13.0", sha256="375f83c8750b0f4dea5b676471e73e94f3710bc3a327ec88b59f25eae1c3a1e8") + + variant("kraken", default=False, description="Enable kraken support") + + depends_on("bedtools2", type="run") + depends_on("blast-plus", type="run") + depends_on("cdhit", type="run") + depends_on("fasttree~openmp", type="run") + depends_on("kraken", type="run", when="+kraken") + depends_on("mafft", type="run") + depends_on("mcl+blast", type="run") + depends_on("parallel", type="run") + depends_on("perl@5.8:", type="run") + depends_on("perl-array-utils", type="run") + depends_on("perl-bioperl", type="run") + depends_on("perl-devel-overloadinfo", type="run") + depends_on("perl-digest-md5-file", type="run") + depends_on("perl-exception-class", type="run") + depends_on("perl-file-find-rule", type="run") + depends_on("perl-file-grep", type="run") + depends_on("perl-file-slurper", type="run") + depends_on("perl-file-which", type="run") + depends_on("perl-graph-readwrite", type="run") + depends_on("perl-graph", type="run") + depends_on("perl-log-log4perl", type="run") + depends_on("perl-moose", type="run") + depends_on("perl-perlio-utf8-strict", type="run") + depends_on("perl-text-csv", type="run") + depends_on("perl-xml-parser", type="run") + depends_on("perl-xml-writer", type="run") + depends_on("prank", type="run") + depends_on("r-ggplot2", type="run") + depends_on("r", type="run") + # roary2svg dependencies + depends_on("perl-data-dumper", type="run") + depends_on("perl-list-moreutils", type="run") + depends_on("perl-svg", type="run") + # roary_plots dependencies + depends_on("python", type="run") + depends_on("py-biopython", type="run") + depends_on("py-numpy", type="run") + depends_on("py-pandas", type="run") + depends_on("py-matplotlib", type="run") + depends_on("py-seaborn", type="run") + + def install(self, spec, prefix): + install_tree(".", prefix) + + def setup_run_environment(self, env): + env.prepend_path("PATH", join_path(prefix, "contrib", "roary2svg")) + env.prepend_path("PATH", join_path(prefix, "contrib", "roary_plots")) + env.prepend_path("PERL5LIB", self.prefix.lib) + + @run_after("install") + def modify_roary_pm(self): + with working_dir(join_path(prefix.lib, "Bio")): + filter_file("use Bio::Perl", "use BioPerl", "Roary.pm", string=True) |